I believe that being clean & sober means getting rid of every substance which has control over you, whether it's prescribed by an MD or not, and not worrying about the rest.
15 years ago I quit smoking cigarettes because I would get bronchitis every winter and was tired of wheezing and feeling like hell all the time.
I've proven to myself that I can't drink alcohol without slipping steadily more and more out of control. I also have a serious addiction to processed carbs.
As far as other drugs go, and their being prescribed or not, this has been my experience:
amphetamines: i've been on a RX for adderall for years now. I always played games with it so I'd have enough to take more than I should when I wanted/needed to. I have now lost my medical insurance so I'm working off my last refill ... and I am slowly weaning myself off this junk. What I hate about it most is how I get to where I can't imagine having to actually do anything but lay around without taking it.
opiates: I've been prescribed more than I needed many times, and worked the system to get as much as possible for recreational purposes. But I am thankful that, given all my other addictions, this never became one of them. when I finally ran out of whatever it was, no big deal moving on from it.
marijuana: I have smoked on and off since high school, having gone more years without it than with it. I am also thankful that I don't seem to be addicted to this drug either. I keep a small amount on hand that I use to help me relax and go to sleep at night. I was never the "wake and bake" type. When I have tried doing that, I am a useless zombie all day - a feeling I don't like. But without it, I don't sleep as well and therefore wind up feeling worse during the day. I do feel that I can be clean and sober and still use cannabis in this way.